.TH gmx-nmens 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-nmens \- Generate an ensemble of structures from the normal modes

.SH SYNOPSIS
gmx nmens [\-v [<.trr/.cpt/...>]] [\-e [<.xvg>]]
          [\-s [<.tpr/.tpb/...>]] [\-n [<.ndx>]] [\-o [<.xtc/.trr/...>]]
          [\-nice <int>] [\-xvg <enum>] [\-temp <real>] [\-seed <int>]
          [\-num <int>] [\-first <int>] [\-last <int>]

.SH DESCRIPTION
\fBgmx nmens\fR generates an ensemble around an average structure in a subspace that is defined by a set of normal modes (eigenvectors). The eigenvectors are assumed to be mass\-weighted. The position along each eigenvector is randomly taken from a Gaussian distribution with variance kT/eigenvalue.

By default the starting eigenvector is set to 7, since the first six normal modes are the translational and rotational degrees of freedom.

.SH OPTIONS
Options to specify input and output files:

.BI "\-v" " [<.trr/.cpt/...>] (eigenvec.trr) (Input)"
    Full precision trajectory: trr cpt trj tng

.BI "\-e" " [<.xvg>] (eigenval.xvg) (Input)"
    xvgr/xmgr file

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Index file

.BI "\-o" " [<.xtc/.trr/...>] (ensemble.xtc) (Output)"
    Trajectory: xtc trr trj gro g96 pdb tng


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-temp" " <real> (300)"
    Temperature in Kelvin

.BI "\-seed" " <int> (-1)"
    Random seed, \-1 generates a seed from time and pid

.BI "\-num" " <int> (100)"
    Number of structures to generate

.BI "\-first" " <int> (7)"
    First eigenvector to use (\-1 is select)

.BI "\-last" " <int> (-1)"
    Last eigenvector to use (\-1 is till the last)


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.